Antimycobacterial cyclic peptide natural products bind and dysregulate stress response chaperones

Antimycobacterial cyclic peptide natural products bind and dysregulate stress response chaperones | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Antimycobacterial cyclic peptide natural products bind and dysregulate stress response chaperones Richard Payne, Isabel Barter, Max Bedding, Joshua Maxwell, Paige Hawkins, and 6 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5493888/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 29 Jan, 2026 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract The protein quality control system is a promising and largely untapped mycobacterial target for the discovery of novel antibiotics. The ClpC1:ClpP1P2 protease is an essential component of the system and is involved in both regulatory and stress-related protein degradation. Several cyclic peptide natural products have been discovered, including ecumicin, the ilamycins and cyclomarin, which bind the ClpC1 chaperone component of the system and possess potent antimycobacterial activity. This has led to significant interest in these molecules, and the ClpC1:ClpP1P2 system more generally, as a bona fide target for the development of new classes of tuberculosis drugs. Utilising cutting edge mass-spectrometry-based proteomics on virulent Mycobacterium tuberculosis H37Rv, we reveal key differences in the mechanism of action for ecumicin, ilamycin E and cyclomarin, with each natural product having distinct effects on the proteome and different consequences for ClpC1 substrate recognition. An additional Clp protein, ClpC2, safeguards the ClpC1:ClpP1P2 complex from obstruction by chaperoning excess unfolded proteins in the event of proteotoxic stress. We show that all three natural products bind ClpC2, with varying affinities, in addition to ClpC1. Notably, we report the significant accumulation of the small heat shock protein, Hsp20, in the presence of ecumicin. A direct binding interaction between Hsp20 and ecumicin is observed that is proposed to stimulate this upregulation. Together, our data reveal that these natural products bind and dysregulate chaperones beyond ClpC1 and dysregulate ClpC1 substrate recognition via distinct mechanisms. This highlights the potential for the development of antimycobacterials that disrupt protein quality control beyond a single protein target. Biological sciences/Chemical biology/Natural products Biological sciences/Chemical biology/Proteomics Proteomics ClpC1 Mycobacterium tuberculosis Ecumicin Ilamycin Cyclomarin Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SuppData1.xlsx Supplementary Dataset 1 SuppData2.xlsx Supplementary Dataset 2 SuppData3.xlsx Supplementary Dataset 3 nrreportingsummaryClpC1NatureCommun.pdf Reporting summary nreditorialpolicychecklistClpC1NatureCommun.pdf Editorial policy checklist ClpC1SuppFiguresTablesMethodsNatureCommunSUBMISSION2011.pdf Supplementary Figures, Tables and Methods Cite Share Download PDF Status: Published Journal Publication published 29 Jan, 2026 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-5493888","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":383252993,"identity":"2ce1d1b6-ad55-47f8-b643-0a4b245b5fec","order_by":0,"name":"Richard 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The ClpC1:ClpP1P2 protease is an essential component of the system and is involved in both regulatory and stress-related protein degradation. Several cyclic peptide natural products have been discovered, including ecumicin, the ilamycins and cyclomarin, which bind the ClpC1 chaperone component of the system and possess potent antimycobacterial activity. This has led to significant interest in these molecules, and the ClpC1:ClpP1P2 system more generally, as a bona fide target for the development of new classes of tuberculosis drugs. Utilising cutting edge mass-spectrometry-based proteomics on virulent Mycobacterium tuberculosis H37Rv, we reveal key differences in the mechanism of action for ecumicin, ilamycin E and cyclomarin, with each natural product having distinct effects on the proteome and different consequences for ClpC1 substrate recognition. An additional Clp protein, ClpC2, safeguards the ClpC1:ClpP1P2 complex from obstruction by chaperoning excess unfolded proteins in the event of proteotoxic stress. We show that all three natural products bind ClpC2, with varying affinities, in addition to ClpC1. Notably, we report the significant accumulation of the small heat shock protein, Hsp20, in the presence of ecumicin. A direct binding interaction between Hsp20 and ecumicin is observed that is proposed to stimulate this upregulation. Together, our data reveal that these natural products bind and dysregulate chaperones beyond ClpC1 and dysregulate ClpC1 substrate recognition via distinct mechanisms. 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